calculcate GC content with sliding window in R

get_gc_content.R

library("seqinr") 
refseq=read.fasta('../Code/Amel_variants/Amel_4.5_scaffolds.fa')


wiggle_output <- file("output5.wig", "a")
printf("track type=print wiggle_0 name=fileName description=fileName\n",file=wiggle_output)
window_size=2000
refseq_names=names(refseq)
for(i in 1:length(refseq)) {
  fasta=refseq[[i]]
  fasta_name=refseq_names[[i]]
  fasta_length=length(fasta)-1
  
  mod_window_size=ifelse(fasta_length<window_size,fasta_length,window_size)
  print(mod_window_size)
  starts <- seq(1, length(fasta)-mod_window_size, by = window_size)
  
  n <- length(starts)    # Find the length of the vector "starts"
  chunkGCs <- numeric(n) # Make a vector of the same length as vector "starts", but just containing zeroes
  printf("variableStep chrom=%s span=%d\n",fasta_name,mod_window_size,file=wiggle_output)
  for (i in 1:n) {
    chunk <- fasta[starts[i]:(starts[i]+mod_window_size-1)]
    chunkGC <- GC(chunk)
    chunkGCs[i] <- chunkGC
    printf("%s %s\n",starts[i],ifelse(is.na(chunkGC),0,chunkGC),file=wiggle_output)
  }
}